/// <summary> /// Set up all outputs (live, console and file) prior to the model run /// </summary> /// <param name="numTimeSteps">The number of time steps in the model run</param> /// <param name="ecosystemModelGrid">The model grid</param> /// <param name="outputFilesSuffix">The suffix to be applied to all output files</param> public void SetupOutputs(uint numTimeSteps, ModelGrid ecosystemModelGrid, string outputFilesSuffix) { Console.WriteLine("Setting up global outputs...\n"); // Set the suffix for all output files _OutputSuffix = outputFilesSuffix + "_Global"; // Create an SDS object to hold total abundance and biomass data BasicOutput = SDSCreator.CreateSDS("netCDF", "BasicOutputs" + _OutputSuffix, _OutputPath); // Create vector to hold the values of the time dimension TimeSteps = new float[numTimeSteps + 1]; // Set the first value to be -1 (this will hold initial outputs) TimeSteps[0] = 0; // Fill other values from 0 (this will hold outputs during the model run) for (int i = 1; i < numTimeSteps + 1; i++) { TimeSteps[i] = i; } // Add basic variables to the output file, dimensioned by time string[] TimeDimension = { "Time step" }; DataConverter.AddVariable(BasicOutput, "Total living biomass", "Kg / km^2", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps); DataConverter.AddVariable(BasicOutput, "Organic matter pool", "Kg / km^2", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps); DataConverter.AddVariable(BasicOutput, "Respiratory CO2 pool", "Kg / km^2", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps); DataConverter.AddVariable(BasicOutput, "Number of cohorts extinct", "", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps); DataConverter.AddVariable(BasicOutput, "Number of cohorts produced", "", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps); DataConverter.AddVariable(BasicOutput, "Number of cohorts combined", "", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps); DataConverter.AddVariable(BasicOutput, "Number of cohorts in model", "", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps); DataConverter.AddVariable(BasicOutput, "Number of stocks in model", "", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps); this.FileName = _OutputPath + "BasicOutputs" + _OutputSuffix + ".nc"; }
/// <summary> /// Set up the predation tracker /// </summary>_ /// <param name="numTimeSteps">The total number of timesteps for this simulation</param> /// <param name="cellIndices">List of indices of active cells in the model grid</param> /// <param name="massFlowsFilename">Filename for outputs of the flows of mass between predators and prey</param> /// <param name="cohortDefinitions">The functional group definitions for cohorts in the model</param> /// <param name="missingValue">The missing value to be used in the output file</param> /// <param name="outputFileSuffix">The suffix to be applied to the output file</param> /// <param name="outputPath">The path to write the output file to</param> /// <param name="trackerMassBins">The mass bin handler containing the mass bins to be used for predation tracking</param> /// <param name="cellIndex">The index of the current cell in the list of all cells to run the model for</param> public PredationTracker(uint numTimeSteps, List <uint[]> cellIndices, string massFlowsFilename, FunctionalGroupDefinitions cohortDefinitions, double missingValue, string outputFileSuffix, string outputPath, MassBinsHandler trackerMassBins, int cellIndex) { // Assign the missing value _MissingValue = missingValue; // Get the mass bins to use for the predation tracker and the number of mass bins that this correpsonds to _MassBins = trackerMassBins.GetSpecifiedMassBins(); _NumMassBins = trackerMassBins.NumMassBins; // Initialise the array to hold data on mass flows between mass bins _MassFlows = new double[_NumMassBins, _NumMassBins]; // Define the model time steps to be used in the output file float[] TimeSteps = new float[numTimeSteps]; for (int i = 1; i <= numTimeSteps; i++) { TimeSteps[i - 1] = i; } // Initialise the data converter DataConverter = new ArraySDSConvert(); // Initialise the SDS object creator SDSCreator = new CreateSDSObject(); // Create an SDS object to hold the predation tracker data MassFlowsDataSet = SDSCreator.CreateSDS("netCDF", massFlowsFilename + outputFileSuffix + "_Cell" + cellIndex, outputPath); // Define the dimensions to be used in the predation tracker output file string[] dimensions = { "Predator mass bin", "Prey mass bin", "Time steps" }; // Add the mass flow variable to the predation tracker DataConverter.AddVariable(MassFlowsDataSet, "Log mass (g)", 3, dimensions, _MissingValue, _MassBins, _MassBins, TimeSteps); }
/// <summary> /// Constructor for the global NPP tracker: sets up the output file and the data arrays /// </summary> /// <param name="outputPath">Path to the file to output NPP data to</param> /// <param name="numLats">The number of cells latitudinally in the NPP output grid</param> /// <param name="numLons">The number of cells longitudinally in the NPP output grid</param> /// <param name="lats">The latitudes of cells in the grid to output</param> /// <param name="lons">The longitudes of cells in the grid to output</param> /// <param name="latCellSize">The latitudinal cell size of the grid to output</param> /// <param name="lonCellSize">The longitudinal cell size of the grid to output</param> /// <param name="numTimeSteps">The number of time steps to output NPP data for</param> public GlobalNPPTracker(string outputPath, int numLats, int numLons, float[] lats, float[] lons, float latCellSize, float lonCellSize, int numTimeSteps, int numStocks) { _NumLats = numLats; _NumLons = numLons; // Initialise the data converter DataConverter = new ArraySDSConvert(); // Initialise the SDS object creator SDSCreator = new CreateSDSObject(); // Create an SDS object to hold NPP data NPPOutput = SDSCreator.CreateSDS("netCDF", "NPPOutput", outputPath); // Create an SDS object to hold total abundance and biomass data HANPPOutput = SDSCreator.CreateSDS("netCDF", "HANPPOutput", outputPath); // Create vector to hold the values of the time dimension float[] TimeSteps = new float[numTimeSteps]; // Fill other values from 0 (this will hold outputs during the model run) for (int i = 0; i < numTimeSteps; i++) { TimeSteps[i] = i; } // Declare vectors for geographical dimension data float[] outLats = new float[numLats]; float[] outLons = new float[numLons]; // Populate the dimension variable vectors with cell centre latitude and longitudes for (int i = 0; i < numLats; i++) { outLats[i] = lats[i] + (latCellSize / 2); } for (int jj = 0; jj < numLons; jj++) { outLons[jj] = lons[jj] + (lonCellSize / 2); } // Add output variables that are dimensioned geographically and temporally to grid output file string[] GeographicalDimensions = { "Latitude", "Longitude", "Time step" }; for (int ii = 0; ii < numStocks; ii++) { DataConverter.AddVariable(NPPOutput, "NPP_" + ii.ToString(), 3, GeographicalDimensions, -9999.0, outLats, outLons, TimeSteps); DataConverter.AddVariable(HANPPOutput, "HANPP_" + ii.ToString(), 3, GeographicalDimensions, -9999.0, outLats, outLons, TimeSteps); } NPP = new double[numLats, numLons, numStocks]; HANPP = new double[numLats, numLons, numStocks]; for (int ii = 0; ii < numLats; ii++) { for (int jj = 0; jj < numLons; jj++) { for (int kk = 0; kk < numStocks; kk++) { NPP[ii, jj, kk] = -9999.0; HANPP[ii, jj, kk] = -9999.0; } } } this.FileName = outputPath + "NPPOutput.nc"; }
public void OutputCurrentModelState(ModelGrid currentModelGrid, FunctionalGroupDefinitions functionalGroupHandler, List <uint[]> cellIndices, uint currentTimestep, int maximumNumberOfCohorts, string filename) { float[] Latitude = currentModelGrid.Lats; float[] Longitude = currentModelGrid.Lons; float[] CohortFunctionalGroup = new float[functionalGroupHandler.GetNumberOfFunctionalGroups()]; for (int fg = 0; fg < CohortFunctionalGroup.Length; fg++) { CohortFunctionalGroup[fg] = fg; } int CellCohortNumber = 0; GridCellCohortHandler CellCohorts; for (int cellIndex = 0; cellIndex < cellIndices.Count; cellIndex++) { CellCohorts = currentModelGrid.GetGridCellCohorts(cellIndices[cellIndex][0], cellIndices[cellIndex][1]); for (int i = 0; i < CellCohorts.Count; i++) { if (CellCohorts[i].Count > CellCohortNumber) { CellCohortNumber = CellCohorts[i].Count; } } } int MaxNumberCohorts = Math.Max(CellCohortNumber, maximumNumberOfCohorts); float[] Cohort = new float[MaxNumberCohorts]; for (int c = 0; c < Cohort.Length; c++) { Cohort[c] = c; } //Define an array for stock functional group - there are only three currently float[] StockFunctionalGroup = new float[] { 1, 2, 3 }; //Define an array for index of stocks - there is only one currently float[] Stock = new float[] { 1 }; string Filename = filename + "_" + currentTimestep.ToString() + Simulation.ToString(); StateOutput = SDSCreator.CreateSDS("netCDF", Filename, _OutputPath); //Define the cohort properties for output string[] CohortProperties = new string[] { "JuvenileMass", "AdultMass", "IndividualBodyMass", "IndividualReproductivePotentialMass", "CohortAbundance", "BirthTimeStep", "MaturityTimeStep", "LogOptimalPreyBodySizeRatio", "MaximumAchievedBodyMass", "Merged", "TrophicIndex", "ProportionTimeActive" }; //define the dimensions for cohort outputs string[] dims = new string[] { "Latitude", "Longitude", "Cohort Functional Group", "Cohort" }; // Add the variables for each cohort property // Then calculate the state for this property and put the data to this variable foreach (string v in CohortProperties) { DataConverter.AddVariable(StateOutput, "Cohort" + v, 4, dims, currentModelGrid.GlobalMissingValue, Latitude, Longitude, CohortFunctionalGroup, Cohort); StateOutput.PutData <double[, , , ]>("Cohort" + v, CalculateCurrentCohortState(currentModelGrid, v, Latitude.Length, Longitude.Length, CohortFunctionalGroup.Length, Cohort.Length, cellIndices)); StateOutput.Commit(); } //Define the stock properties for output string[] StockProperties = new string[] { "IndividualBodyMass", "TotalBiomass" }; //define the dimensions for cohort outputs dims = new string[] { "Latitude", "Longitude", "Stock Functional Group", "Stock" }; // Add the variables for each stock property // Then calculate the state for this property and put the data to this variable foreach (string v in StockProperties) { DataConverter.AddVariable(StateOutput, "Stock" + v, 4, dims, currentModelGrid.GlobalMissingValue, Latitude, Longitude, StockFunctionalGroup, Stock); StateOutput.PutData <double[, , , ]>("Stock" + v, CalculateCurrentStockState(currentModelGrid, v, Latitude.Length, Longitude.Length, StockFunctionalGroup.Length, Stock.Length, cellIndices)); StateOutput.Commit(); } //Close this data set StateOutput.Dispose(); }
/// <summary> /// Set up the predation tracker /// </summary>_ /// <param name="numTimeSteps">The total number of timesteps for this simulation</param> /// <param name="cellIndices">List of indices of active cells in the model grid</param> /// <param name="massFlowsFilename">Filename for outputs of the flows of mass between predators and prey</param> /// <param name="cohortDefinitions">The functional group definitions for cohorts in the model</param> /// <param name="missingValue">The missing value to be used in the output file</param> /// <param name="outputFileSuffix">The suffix to be applied to the output file</param> /// <param name="outputPath">The path to write the output file to</param> /// <param name="trackerMassBins">The mass bin handler containing the mass bins to be used for predation tracking</param> /// <param name="cellIndex">The index of the current cell in the list of all cells to run the model for</param> public PredationTracker(uint numTimeSteps, List<uint[]> cellIndices, string massFlowsFilename, FunctionalGroupDefinitions cohortDefinitions, double missingValue, string outputFileSuffix, string outputPath, MassBinsHandler trackerMassBins, int cellIndex) { // Assign the missing value _MissingValue = missingValue; // Get the mass bins to use for the predation tracker and the number of mass bins that this correpsonds to _MassBins = trackerMassBins.GetSpecifiedMassBins(); _NumMassBins = trackerMassBins.NumMassBins; // Initialise the array to hold data on mass flows between mass bins _MassFlows = new double[_NumMassBins, _NumMassBins]; // Define the model time steps to be used in the output file float[] TimeSteps = new float[numTimeSteps]; for (int i = 1; i <= numTimeSteps; i++) { TimeSteps[i - 1] = i; } // Initialise the data converter DataConverter = new ArraySDSConvert(); // Initialise the SDS object creator SDSCreator = new CreateSDSObject(); // Create an SDS object to hold the predation tracker data MassFlowsDataSet = SDSCreator.CreateSDS("netCDF", massFlowsFilename + outputFileSuffix + "_Cell" + cellIndex, outputPath); // Define the dimensions to be used in the predation tracker output file string[] dimensions = { "Predator mass bin", "Prey mass bin", "Time steps" }; // Add the mass flow variable to the predation tracker DataConverter.AddVariable(MassFlowsDataSet, "Log mass (g)", 3, dimensions, _MissingValue, _MassBins, _MassBins, TimeSteps); }
/// <summary> /// Constructor for the global NPP tracker: sets up the output file and the data arrays /// </summary> /// <param name="outputPath">Path to the file to output NPP data to</param> /// <param name="numLats">The number of cells latitudinally in the NPP output grid</param> /// <param name="numLons">The number of cells longitudinally in the NPP output grid</param> /// <param name="lats">The latitudes of cells in the grid to output</param> /// <param name="lons">The longitudes of cells in the grid to output</param> /// <param name="latCellSize">The latitudinal cell size of the grid to output</param> /// <param name="lonCellSize">The longitudinal cell size of the grid to output</param> /// <param name="numTimeSteps">The number of time steps to output NPP data for</param> public GlobalNPPTracker(string outputPath, int numLats, int numLons, float[] lats, float[] lons, float latCellSize, float lonCellSize, int numTimeSteps, int numStocks) { _NumLats = numLats; _NumLons = numLons; // Initialise the data converter DataConverter = new ArraySDSConvert(); // Initialise the SDS object creator SDSCreator = new CreateSDSObject(); // Create an SDS object to hold NPP data NPPOutput = SDSCreator.CreateSDS("netCDF", "NPPOutput", outputPath); // Create an SDS object to hold total abundance and biomass data HANPPOutput = SDSCreator.CreateSDS("netCDF", "HANPPOutput", outputPath); // Create vector to hold the values of the time dimension float[] TimeSteps = new float[numTimeSteps]; // Fill other values from 0 (this will hold outputs during the model run) for (int i = 0; i < numTimeSteps; i++) { TimeSteps[i] = i; } // Declare vectors for geographical dimension data float[] outLats = new float[numLats]; float[] outLons = new float[numLons]; // Populate the dimension variable vectors with cell centre latitude and longitudes for (int i = 0; i < numLats; i++) { outLats[i] = lats[i] + (latCellSize / 2); } for (int jj = 0; jj < numLons; jj++) { outLons[jj] = lons[jj] + (lonCellSize / 2); } // Add output variables that are dimensioned geographically and temporally to grid output file string[] GeographicalDimensions = { "Latitude", "Longitude", "Time step" }; for (int ii = 0; ii < numStocks; ii++) { DataConverter.AddVariable(NPPOutput, "NPP_" + ii.ToString(), 3, GeographicalDimensions, -9999.0, outLats, outLons, TimeSteps); DataConverter.AddVariable(HANPPOutput, "HANPP_" + ii.ToString(), 3, GeographicalDimensions, -9999.0, outLats, outLons, TimeSteps); } NPP = new double[numLats, numLons, numStocks]; HANPP = new double[numLats, numLons, numStocks]; for (int ii = 0; ii < numLats; ii++) { for (int jj = 0; jj < numLons; jj++) { for (int kk = 0; kk < numStocks; kk++) { NPP[ii, jj, kk] = -9999.0; HANPP[ii, jj, kk] = -9999.0; } } } this.FileName = outputPath + "NPPOutput.nc"; }
public void SetupOutputs(ModelGrid ecosystemModelGrid, string outputFilesSuffix, uint numTimeSteps, FunctionalGroupDefinitions cohortFunctionalGroupDefinitions, FunctionalGroupDefinitions stockFunctionalGroupDefinitions) { // Create an SDS object to hold grid outputs GridOutput = SDSCreator.CreateSDS("netCDF", "GridOutputs" + outputFilesSuffix, _OutputPath); // Initilalise trait-based outputs InitialiseTraitBasedOutputs(cohortFunctionalGroupDefinitions, stockFunctionalGroupDefinitions); // Create vector to hold the values of the time dimension TimeSteps = new float[numTimeSteps + 1]; // Set the first value to be 0 (this will hold initial outputs) TimeSteps[0] = 0; // Fill other values from 0 (this will hold outputs during the model run) for (int i = 1; i < numTimeSteps + 1; i++) { TimeSteps[i] = i; } // Declare vectors for geographical dimension data float[] outLats = new float[ecosystemModelGrid.NumLatCells]; float[] outLons = new float[ecosystemModelGrid.NumLonCells]; // Populate the dimension variable vectors with cell centre latitude and longitudes for (int i = 0; i < ecosystemModelGrid.NumLatCells; i++) { outLats[i] = ecosystemModelGrid.Lats[i] + (ecosystemModelGrid.LatCellSize / 2); } for (int jj = 0; jj < ecosystemModelGrid.NumLonCells; jj++) { outLons[jj] = ecosystemModelGrid.Lons[jj] + (ecosystemModelGrid.LonCellSize / 2); } //GridOutputArray = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells, numTimeSteps]; // Add output variables that are dimensioned geographically and temporally to grid output file string[] GeographicalDimensions = { "Latitude", "Longitude", "Time step" }; DataConverter.AddVariable(GridOutput, "Biomass density", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps); DataConverter.AddVariable(GridOutput, "Abundance density", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps); // Initialise the arrays that will be used for the grid-based outputs LogBiomassDensityGridCohorts = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells]; LogBiomassDensityGridStocks = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells]; LogBiomassDensityGrid = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells]; LogAbundanceDensityGridCohorts = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells]; FrostDays = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells]; FracEvergreen = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells]; Realm = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells]; HANPP = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells]; Temperature = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells]; // Temporary outputs for checking plant model DataConverter.AddVariable(GridOutput, "Fraction year frost", 3, GeographicalDimensions, ecosystemModelGrid.GlobalMissingValue, outLats, outLons, TimeSteps); DataConverter.AddVariable(GridOutput, "Fraction evergreen", 3, GeographicalDimensions, ecosystemModelGrid.GlobalMissingValue, outLats, outLons, TimeSteps); DataConverter.AddVariable(GridOutput, "Realm", 3, GeographicalDimensions, ecosystemModelGrid.GlobalMissingValue, outLats, outLons, TimeSteps); DataConverter.AddVariable(GridOutput, "HANPP", 3, GeographicalDimensions, ecosystemModelGrid.GlobalMissingValue, outLats, outLons, TimeSteps); DataConverter.AddVariable(GridOutput, "Temperature", 3, GeographicalDimensions, ecosystemModelGrid.GlobalMissingValue, outLats, outLons, TimeSteps); // Set up outputs for medium or high output levels if ((ModelOutputDetail == OutputDetailLevel.Medium) || (ModelOutputDetail == OutputDetailLevel.High)) { double[,] temp = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells]; foreach (string TraitValue in CohortTraitIndices.Keys) { BiomassDensityGrid.Add(TraitValue, temp); DataConverter.AddVariable(GridOutput, TraitValue + "biomass density", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps); AbundanceDensityGrid.Add(TraitValue, temp); DataConverter.AddVariable(GridOutput, TraitValue + "abundance density", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps); } foreach (string TraitValue in StockTraitIndices.Keys) { BiomassDensityGrid.Add(TraitValue, temp); DataConverter.AddVariable(GridOutput, TraitValue + "biomass density", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps); } if (OutputMetrics) { double[,] MTL = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells]; MetricsGrid.Add("Mean Trophic Level", MTL); double[,] TE = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells]; MetricsGrid.Add("Trophic Evenness", TE); double[,] BE = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells]; MetricsGrid.Add("Biomass Evenness", BE); double[,] FR = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells]; MetricsGrid.Add("Functional Richness", FR); double[,] RFE = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells]; MetricsGrid.Add("Rao Functional Evenness", RFE); double[,] BR = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells]; MetricsGrid.Add("Biomass Richness", BR); double[,] TR = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells]; MetricsGrid.Add("Trophic Richness", TR); double[,] Bmax = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells]; MetricsGrid.Add("Max Bodymass", Bmax); double[,] Bmin = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells]; MetricsGrid.Add("Min Bodymass", Bmin); double[,] TImax = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells]; MetricsGrid.Add("Max Trophic Index", TImax); double[,] TImin = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells]; MetricsGrid.Add("Min Trophic Index", TImin); double[,] ArithMean = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells]; MetricsGrid.Add("Arithmetic Mean Bodymass", ArithMean); double[,] GeomMean = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells]; MetricsGrid.Add("Geometric Mean Bodymass", GeomMean); DataConverter.AddVariable(GridOutput, "Mean Trophic Level", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps); DataConverter.AddVariable(GridOutput, "Trophic Evenness", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps); DataConverter.AddVariable(GridOutput, "Biomass Evenness", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps); DataConverter.AddVariable(GridOutput, "Functional Richness", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps); DataConverter.AddVariable(GridOutput, "Rao Functional Evenness", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps); DataConverter.AddVariable(GridOutput, "Biomass Richness", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps); DataConverter.AddVariable(GridOutput, "Trophic Richness", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps); DataConverter.AddVariable(GridOutput, "Max Bodymass", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps); DataConverter.AddVariable(GridOutput, "Min Bodymass", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps); DataConverter.AddVariable(GridOutput, "Max Trophic Index", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps); DataConverter.AddVariable(GridOutput, "Min Trophic Index", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps); DataConverter.AddVariable(GridOutput, "Arithmetic Mean Bodymass", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps); DataConverter.AddVariable(GridOutput, "Geometric Mean Bodymass", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps); } } }
public void WriteFeedingInteractions(uint timestep) { int nrows = FeedingInteractionsMatrixPredation.GetLength(0); int ncols = FeedingInteractionsMatrixPredation.GetLength(1); int MaxLengthPredation = 0; for (int i = 0; i < nrows; i++) { for (int j = 0; j < ncols; j++) { if (FeedingInteractionsMatrixPredation[i, j].Count > MaxLengthPredation) MaxLengthPredation = FeedingInteractionsMatrixPredation[i, j].Count; } } double[, ,] FGIndicesPredation = new double[nrows, ncols, MaxLengthPredation]; double[, ,] FGIndicesHerbivory = new double[nrows, ncols, 2]; double[, ,] CIndicesPredation = new double[nrows, ncols, MaxLengthPredation]; double[, ,] CIndicesHerbivory = new double[nrows, ncols, 2]; double[, ,] BiomassAssimilatedPredation = new double[nrows, ncols, MaxLengthPredation]; double[, ,] BiomassAssimilatedHerbivory = new double[nrows, ncols, 2]; double[, ,] BiomassIngestedPredation = new double[nrows, ncols, MaxLengthPredation]; double[, ,] BiomassIngestedHerbivory = new double[nrows, ncols, 2]; float[] FGIndices = new float[nrows]; float[] CIndices = new float[ncols]; float[] PredationIndices = new float[MaxLengthPredation]; float[] HerbivoryIndices = new float[2] {0,1}; for (int i = 0; i < nrows; i++) { FGIndices[i] = i; } for (int i = 0; i < ncols; i++) { CIndices[i] = i; } for (int i = 0; i < MaxLengthPredation; i++) { PredationIndices[i] = i; } for (int f = 0; f < nrows; f++) { for (int c = 0; c < ncols; c++) { //Populate output data matrices for predation feeding events for (int i = 0; i < FeedingInteractionsMatrixPredation[f, c].Count; i++) { FGIndicesPredation[f, c, i] = Convert.ToDouble(FeedingInteractionsMatrixPredation[f, c].ElementAt(i).Item1); CIndicesPredation[f, c, i] = Convert.ToDouble(FeedingInteractionsMatrixPredation[f, c].ElementAt(i).Item2); BiomassAssimilatedPredation[f, c, i] = (FeedingInteractionsMatrixPredation[f, c].ElementAt(i).Item3); BiomassIngestedPredation[f, c, i] = (FeedingInteractionsMatrixPredation[f, c].ElementAt(i).Item4); } //Populate output data matrices for herbivory feeding events for (int i = 0; i < FeedingInteractionsMatrixHerbivory[f,c].Count; i++) { FGIndicesHerbivory[f, c, i] = Convert.ToDouble(FeedingInteractionsMatrixHerbivory[f, c].ElementAt(i).Item1); CIndicesHerbivory[f, c, i] = Convert.ToDouble(FeedingInteractionsMatrixHerbivory[f, c].ElementAt(i).Item2); BiomassAssimilatedHerbivory[f, c, i] = (FeedingInteractionsMatrixHerbivory[f, c].ElementAt(i).Item3); BiomassIngestedHerbivory[f, c, i] = (FeedingInteractionsMatrixHerbivory[f, c].ElementAt(i).Item4); } } } // Initialise the data converter DataConverter = new ArraySDSConvert(); // Initialise the SDS object creator SDSCreator = new CreateSDSObject(); // Create an SDS object to hold the predation tracker data _FeedingInteractionsDS = SDSCreator.CreateSDS("netCDF", _Filename + _OutputFileSuffix + timestep, _OutputPath); string[] PredationDimensions = new string[3] {"Functional Group Indices","Cohort Indices","Predation Interaction Dimension"}; string[] HerbivoryDimensions = new string[3] { "Functional Group Indices", "Cohort Indices", "Herbivory Interaction Dimension" }; string[] PredD1 = new string [1] { PredationDimensions[0] }; string[] PredD2 = new string[1] { PredationDimensions[1] }; string[] PredD3 = new string[1] { PredationDimensions[2] }; string[] HerbD3 = new string[1] { HerbivoryDimensions[2] }; DataConverter.AddVariable(_FeedingInteractionsDS, PredationDimensions[0], "index", 1, PredD1, _MV, FGIndices); DataConverter.AddVariable(_FeedingInteractionsDS, PredationDimensions[1], "index", 1, PredD2, _MV, CIndices); DataConverter.AddVariable(_FeedingInteractionsDS, PredationDimensions[2], "index", 1, PredD3, _MV, PredationIndices); DataConverter.AddVariable(_FeedingInteractionsDS, HerbivoryDimensions[2], "index", 1, HerbD3, _MV, HerbivoryIndices); /*DataConverter.AddVariable(_FeedingInteractionsDS, "Predation Interactions Functional Groups", 3, PredationDimensions, _MV, FGIndices, CIndices, PredationIndices); DataConverter.AddVariable(_FeedingInteractionsDS, "Predation Interactions Cohort Index", 3, PredationDimensions, _MV, FGIndices, CIndices, PredationIndices); DataConverter.AddVariable(_FeedingInteractionsDS, "Predation Interactions Biomass Assimilated", 3, PredationDimensions, _MV, FGIndices, CIndices, PredationIndices); DataConverter.AddVariable(_FeedingInteractionsDS, "Predation Interactions Biomass Ingested", 3, PredationDimensions, _MV, FGIndices, CIndices, PredationIndices); DataConverter.AddVariable(_FeedingInteractionsDS, "Herbivory Interactions Functional Groups", 3, HerbivoryDimensions, _MV, FGIndices, CIndices, HerbivoryIndices); DataConverter.AddVariable(_FeedingInteractionsDS, "Herbivory Interactions Stock Index", 3, HerbivoryDimensions, _MV, FGIndices, CIndices, HerbivoryIndices); DataConverter.AddVariable(_FeedingInteractionsDS, "Herbivory Interactions Biomass Assimilated", 3, HerbivoryDimensions, _MV, FGIndices, CIndices, HerbivoryIndices); DataConverter.AddVariable(_FeedingInteractionsDS, "Herbivory Interactions Biomass Ingested", 3, HerbivoryDimensions, _MV, FGIndices, CIndices, HerbivoryIndices);*/ //Add variable to SDS var FGIPredOut = _FeedingInteractionsDS.AddVariable<double>("Predation Interactions Functional Groups", FGIndicesPredation, PredationDimensions); FGIPredOut.Metadata["DisplayName"] = "Predation Interactions Functional Groups"; FGIPredOut.Metadata["MissingValue"] = _MV; //Add variable to SDS var CIPredOut = _FeedingInteractionsDS.AddVariable<double>("Predation Interactions Cohort Index", CIndicesPredation, PredationDimensions); CIPredOut.Metadata["DisplayName"] = "Predation Interactions Cohort Index"; CIPredOut.Metadata["MissingValue"] = _MV; //Add variable to SDS var BAPredOut = _FeedingInteractionsDS.AddVariable<double>("Predation Interactions Biomass Assimilated", BiomassAssimilatedPredation, PredationDimensions); BAPredOut.Metadata["DisplayName"] = "Predation Interactions Biomass Assimilated"; BAPredOut.Metadata["MissingValue"] = _MV; //Add variable to SDS var BIPredOut = _FeedingInteractionsDS.AddVariable<double>("Predation Interactions Biomass Ingested", BiomassIngestedPredation, PredationDimensions); BIPredOut.Metadata["DisplayName"] = "Predation Interactions Biomass Ingested"; BIPredOut.Metadata["MissingValue"] = _MV; //Add variable to SDS var FGIHerbOut = _FeedingInteractionsDS.AddVariable<double>("Herbivory Interactions Functional Groups", FGIndicesHerbivory, HerbivoryDimensions); FGIHerbOut.Metadata["DisplayName"] = "Herbivory Interactions Functional Groups"; FGIHerbOut.Metadata["MissingValue"] = _MV; //Add variable to SDS var CIHerbOut = _FeedingInteractionsDS.AddVariable<double>("Herbivory Interactions Cohort Index", CIndicesHerbivory, HerbivoryDimensions); CIHerbOut.Metadata["DisplayName"] = "Herbivory Interactions Cohort Index"; CIHerbOut.Metadata["MissingValue"] = _MV; //Add variable to SDS var BAHerbOut = _FeedingInteractionsDS.AddVariable<double>("Herbivory Interactions Biomass Assimilated", BiomassAssimilatedHerbivory, HerbivoryDimensions); BAHerbOut.Metadata["DisplayName"] = "Herbivory Interactions Biomass Assimilated"; BAHerbOut.Metadata["MissingValue"] = _MV; //Add variable to SDS var BIHerbOut = _FeedingInteractionsDS.AddVariable<double>("Herbivory Interactions Biomass Ingested", BiomassIngestedHerbivory, HerbivoryDimensions); BIHerbOut.Metadata["DisplayName"] = "Herbivory Interactions Biomass Ingested"; BIHerbOut.Metadata["MissingValue"] = _MV; //Commit changes _FeedingInteractionsDS.Commit(); }
public void WriteFeedingInteractions(uint timestep) { int nrows = FeedingInteractionsMatrixPredation.GetLength(0); int ncols = FeedingInteractionsMatrixPredation.GetLength(1); int MaxLengthPredation = 0; for (int i = 0; i < nrows; i++) { for (int j = 0; j < ncols; j++) { if (FeedingInteractionsMatrixPredation[i, j].Count > MaxLengthPredation) { MaxLengthPredation = FeedingInteractionsMatrixPredation[i, j].Count; } } } double[, ,] FGIndicesPredation = new double[nrows, ncols, MaxLengthPredation]; double[, ,] FGIndicesHerbivory = new double[nrows, ncols, 2]; double[, ,] CIndicesPredation = new double[nrows, ncols, MaxLengthPredation]; double[, ,] CIndicesHerbivory = new double[nrows, ncols, 2]; double[, ,] BiomassAssimilatedPredation = new double[nrows, ncols, MaxLengthPredation]; double[, ,] BiomassAssimilatedHerbivory = new double[nrows, ncols, 2]; double[, ,] BiomassIngestedPredation = new double[nrows, ncols, MaxLengthPredation]; double[, ,] BiomassIngestedHerbivory = new double[nrows, ncols, 2]; float[] FGIndices = new float[nrows]; float[] CIndices = new float[ncols]; float[] PredationIndices = new float[MaxLengthPredation]; float[] HerbivoryIndices = new float[2] { 0, 1 }; for (int i = 0; i < nrows; i++) { FGIndices[i] = i; } for (int i = 0; i < ncols; i++) { CIndices[i] = i; } for (int i = 0; i < MaxLengthPredation; i++) { PredationIndices[i] = i; } for (int f = 0; f < nrows; f++) { for (int c = 0; c < ncols; c++) { //Populate output data matrices for predation feeding events for (int i = 0; i < FeedingInteractionsMatrixPredation[f, c].Count; i++) { FGIndicesPredation[f, c, i] = Convert.ToDouble(FeedingInteractionsMatrixPredation[f, c].ElementAt(i).Item1); CIndicesPredation[f, c, i] = Convert.ToDouble(FeedingInteractionsMatrixPredation[f, c].ElementAt(i).Item2); BiomassAssimilatedPredation[f, c, i] = (FeedingInteractionsMatrixPredation[f, c].ElementAt(i).Item3); BiomassIngestedPredation[f, c, i] = (FeedingInteractionsMatrixPredation[f, c].ElementAt(i).Item4); } //Populate output data matrices for herbivory feeding events for (int i = 0; i < FeedingInteractionsMatrixHerbivory[f, c].Count; i++) { FGIndicesHerbivory[f, c, i] = Convert.ToDouble(FeedingInteractionsMatrixHerbivory[f, c].ElementAt(i).Item1); CIndicesHerbivory[f, c, i] = Convert.ToDouble(FeedingInteractionsMatrixHerbivory[f, c].ElementAt(i).Item2); BiomassAssimilatedHerbivory[f, c, i] = (FeedingInteractionsMatrixHerbivory[f, c].ElementAt(i).Item3); BiomassIngestedHerbivory[f, c, i] = (FeedingInteractionsMatrixHerbivory[f, c].ElementAt(i).Item4); } } } // Initialise the data converter DataConverter = new ArraySDSConvert(); // Initialise the SDS object creator SDSCreator = new CreateSDSObject(); // Create an SDS object to hold the predation tracker data _FeedingInteractionsDS = SDSCreator.CreateSDS("netCDF", _Filename + _OutputFileSuffix + timestep, _OutputPath); string[] PredationDimensions = new string[3] { "Functional Group Indices", "Cohort Indices", "Predation Interaction Dimension" }; string[] HerbivoryDimensions = new string[3] { "Functional Group Indices", "Cohort Indices", "Herbivory Interaction Dimension" }; string[] PredD1 = new string [1] { PredationDimensions[0] }; string[] PredD2 = new string[1] { PredationDimensions[1] }; string[] PredD3 = new string[1] { PredationDimensions[2] }; string[] HerbD3 = new string[1] { HerbivoryDimensions[2] }; DataConverter.AddVariable(_FeedingInteractionsDS, PredationDimensions[0], "index", 1, PredD1, _MV, FGIndices); DataConverter.AddVariable(_FeedingInteractionsDS, PredationDimensions[1], "index", 1, PredD2, _MV, CIndices); DataConverter.AddVariable(_FeedingInteractionsDS, PredationDimensions[2], "index", 1, PredD3, _MV, PredationIndices); DataConverter.AddVariable(_FeedingInteractionsDS, HerbivoryDimensions[2], "index", 1, HerbD3, _MV, HerbivoryIndices); /*DataConverter.AddVariable(_FeedingInteractionsDS, "Predation Interactions Functional Groups", 3, PredationDimensions, _MV, FGIndices, CIndices, PredationIndices); * DataConverter.AddVariable(_FeedingInteractionsDS, "Predation Interactions Cohort Index", 3, PredationDimensions, _MV, FGIndices, CIndices, PredationIndices); * DataConverter.AddVariable(_FeedingInteractionsDS, "Predation Interactions Biomass Assimilated", 3, PredationDimensions, _MV, FGIndices, CIndices, PredationIndices); * DataConverter.AddVariable(_FeedingInteractionsDS, "Predation Interactions Biomass Ingested", 3, PredationDimensions, _MV, FGIndices, CIndices, PredationIndices); * * DataConverter.AddVariable(_FeedingInteractionsDS, "Herbivory Interactions Functional Groups", 3, HerbivoryDimensions, _MV, FGIndices, CIndices, HerbivoryIndices); * DataConverter.AddVariable(_FeedingInteractionsDS, "Herbivory Interactions Stock Index", 3, HerbivoryDimensions, _MV, FGIndices, CIndices, HerbivoryIndices); * DataConverter.AddVariable(_FeedingInteractionsDS, "Herbivory Interactions Biomass Assimilated", 3, HerbivoryDimensions, _MV, FGIndices, CIndices, HerbivoryIndices); * DataConverter.AddVariable(_FeedingInteractionsDS, "Herbivory Interactions Biomass Ingested", 3, HerbivoryDimensions, _MV, FGIndices, CIndices, HerbivoryIndices);*/ //Add variable to SDS var FGIPredOut = _FeedingInteractionsDS.AddVariable <double>("Predation Interactions Functional Groups", FGIndicesPredation, PredationDimensions); FGIPredOut.Metadata["DisplayName"] = "Predation Interactions Functional Groups"; FGIPredOut.Metadata["MissingValue"] = _MV; //Add variable to SDS var CIPredOut = _FeedingInteractionsDS.AddVariable <double>("Predation Interactions Cohort Index", CIndicesPredation, PredationDimensions); CIPredOut.Metadata["DisplayName"] = "Predation Interactions Cohort Index"; CIPredOut.Metadata["MissingValue"] = _MV; //Add variable to SDS var BAPredOut = _FeedingInteractionsDS.AddVariable <double>("Predation Interactions Biomass Assimilated", BiomassAssimilatedPredation, PredationDimensions); BAPredOut.Metadata["DisplayName"] = "Predation Interactions Biomass Assimilated"; BAPredOut.Metadata["MissingValue"] = _MV; //Add variable to SDS var BIPredOut = _FeedingInteractionsDS.AddVariable <double>("Predation Interactions Biomass Ingested", BiomassIngestedPredation, PredationDimensions); BIPredOut.Metadata["DisplayName"] = "Predation Interactions Biomass Ingested"; BIPredOut.Metadata["MissingValue"] = _MV; //Add variable to SDS var FGIHerbOut = _FeedingInteractionsDS.AddVariable <double>("Herbivory Interactions Functional Groups", FGIndicesHerbivory, HerbivoryDimensions); FGIHerbOut.Metadata["DisplayName"] = "Herbivory Interactions Functional Groups"; FGIHerbOut.Metadata["MissingValue"] = _MV; //Add variable to SDS var CIHerbOut = _FeedingInteractionsDS.AddVariable <double>("Herbivory Interactions Cohort Index", CIndicesHerbivory, HerbivoryDimensions); CIHerbOut.Metadata["DisplayName"] = "Herbivory Interactions Cohort Index"; CIHerbOut.Metadata["MissingValue"] = _MV; //Add variable to SDS var BAHerbOut = _FeedingInteractionsDS.AddVariable <double>("Herbivory Interactions Biomass Assimilated", BiomassAssimilatedHerbivory, HerbivoryDimensions); BAHerbOut.Metadata["DisplayName"] = "Herbivory Interactions Biomass Assimilated"; BAHerbOut.Metadata["MissingValue"] = _MV; //Add variable to SDS var BIHerbOut = _FeedingInteractionsDS.AddVariable <double>("Herbivory Interactions Biomass Ingested", BiomassIngestedHerbivory, HerbivoryDimensions); BIHerbOut.Metadata["DisplayName"] = "Herbivory Interactions Biomass Ingested"; BIHerbOut.Metadata["MissingValue"] = _MV; //Commit changes _FeedingInteractionsDS.Commit(); }